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Nucleic acids and chromatin

2 The molecular structure of nucleic acids

2.1 The primary structure of nucleic acids

We now know the detail of the order of individual bases, i.e. the genome sequence, of many of the organisms listed in Table 1. In Section 2 we will focus on the structures of nucleic acids within the cell, and we will start this discussion by outlining some of the general principles that apply to all nucleic acid structures.

Nucleic acids found in the cell have primary structures that arise from the directional polymerisation of single nucleotide units. The links between each nucleotide are formed by esterification reactions between the sugar's C3′ hydroxyl group and the -phosphate of an incoming nucleoside triphosphate (NTP) to form a phosphoester linkage, which is shown in Figure 3. The sugar is ribose in the case of RNA, deoxyribose in DNA. This polymerisation process leaves a free hydroxyl on the incoming nucleotide (on the 3′ C of the sugar) to serve for the next reaction in chain elongation.

SAQ 2

What provides the energy for this reaction to proceed?

Answer

Each NTP molecule carries two phosphoanhydride bonds in its triphosphate unit, one of which provides the energy to drive this reaction.

Figure 3 A schematic representation of a nucleic acid backbone. (a) A side view showing the spacing between the bases. (b) Backbone structure (DNA in this case), highlighting the nucleotide units and the phosphoester linkages. Bases are represented by their initial letter. Note that rotation is possible around five bonds in the sugar-phosphate backbone.

The resultant phosphodiester–sugar backbone consists of what are commonly called 5′–3′ (pronounced ‘five-prime to three-prime’) linkages, where the prime refers to the carbon atoms of the sugar unit, as shown in Figure 3b. Thus the 5′ C of one sugar is linked, via a phosphate group (called a phosphodiester group in this context) , to the 3′ C of the next sugar. The bases are joined to the sugar via their N1 position in the case of the pyrimidines (thymine, cytosine or uracil) or their N9 position in the case of the purines (adenine and guanine) Figure 4.

The molecular natures of the nucleic components, the sugar, the phosphate and the base, exert a major influence over both the structures and functions of the macromolecular nucleic acids that comprise them.

SAQ 3

What properties of the three nucleotide components (phosphate, sugar, base), can you predict from their molecular structures?

Answer

The phosphates and sugars carry polarised bonds, so are hydrophilic in nature. In contrast, the bases, which are primarily rich in carbon-carbon and carbon-hydrogen linkages, have fewer polarised bonds and are more hydrophobic.

SAQ 4

From this knowledge of nucleotide chemistry, what would you predict about the higher-order structure of a polynucleotide chain in the physiological conditions found within a cell? (Hint: think of how proteins behave.)

Answer

Such structures would most likely carry the bases buried within the inside, allowing hydrophobic interactions between them, and with the hydrophilic sugar-phosphate backbone on the outside.

Nucleic acids adopt a level of structure analogous to that of protein secondary structure, and just as the chemical properties of the constituent amino acid residues affect the conformation of a protein, so the chemical properties of nucleotides affect nucleic acid secondary structure. We will discuss how the secondary structure of nucleic acids depends on the chemistry of the constituent nucleotides, later in this unit.

Once incorporated into nucleic acids, the five common bases can also be modified by specific enzymes. Some examples of modified bases are shown in Figure 4b and c. These modifications provide additional structural components of nucleic acids and, to a certain extent, provide variety comparable with that found in proteins and polysaccharides. Modified nucleotides serve as recognition features on nucleic acid chains – particularly DNA – for the binding of other macromolecules. The only modification commonly found within DNA is that of methylation, and methylated bases are observed in many organisms. For example, many bacteria contain methylated adenine, which serves to distinguish the genomic DNA from viral non-methylated DNA. In many eukaryotes, the methylation of cytosine is associated with alterations in transcriptional competence. Post-transcriptional modification of RNA nucleotides is particularly common.

Figure 4 The structures of the individual components of nucleic acids, (a) The five common bases and the sugar components in nucleic acids: deoxyribose in DNA and ribose in RNA. Bases are joined to the sugar via N1 (pyrimidine) and N9 (purine). In some cases, bases in nucleic acids are covalently modified post-transcriptionally. The addition of a methyl group (highlighted here in purple) is a common modification. Some of the modified nucleosides found in (b) RNA and (c) DNA are shown here: 5﻿-﻿methylcytidine is often found in eukaryote DNA, while N﻿6﻿-﻿methyladenosine is present in many bacterial DNAs.

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